7P4S

BROMODOMAIN OF HUMAN TAF1 (2) WITH naphthyridinone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Optimization of Naphthyridones into Selective TATA-Binding Protein Associated Factor 1 (TAF1) Bromodomain Inhibitors.

Clegg, M.A.Theodoulou, N.H.Bamborough, P.Chung, C.W.Craggs, P.D.Demont, E.H.Gordon, L.J.Liwicki, G.M.Phillipou, A.Tomkinson, N.C.O.Prinjha, R.K.Humphreys, P.G.

(2021) ACS Med Chem Lett 12: 1308-1317

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00294
  • Primary Citation of Related Structures:  
    7P4S

  • PubMed Abstract: 

    Bromodomain containing proteins and the acetyl-lysine binding bromodomains contained therein are increasingly attractive targets for the development of novel epigenetic therapeutics. To help validate this target class and unravel the complex associated biology, there has been a concerted effort to develop selective small molecule bromodomain inhibitors. Herein we describe the structure-based efforts and multiple challenges encountered in optimizing a naphthyridone template into selective TAF1(2) bromodomain inhibitors which, while unsuitable as chemical probes themselves, show promise for the future development of small molecules to interrogate TAF1(2) biology. Key to this work was the introduction and modulation of the basicity of a pendant amine which had a substantial impact on not only bromodomain selectivity but also cellular target engagement.


  • Organizational Affiliation

    GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2a of Transcription initiation factor TFIID subunit 1137Homo sapiensMutation(s): 0 
Gene Names: TAF1BA2RCCG1CCGSTAF2A
EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21675 (Homo sapiens)
Explore P21675 
Go to UniProtKB:  P21675
PHAROS:  P21675
GTEx:  ENSG00000147133 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21675
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5LV (Subject of Investigation/LOI)
Query on 5LV

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
8-[[1-(3-azanylpropyl)piperidin-4-yl]amino]-5-[5-(hydroxymethyl)pyridin-3-yl]-3-methyl-1~{H}-1,7-naphthyridin-2-one
C23 H30 N6 O2
WQPQQRVHJTZSFA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.651α = 90
b = 56.007β = 90
c = 58.308γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-10-13 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description